Knowledge about the importance of physical habitat characteristics to the breeding site selection of birds is a prerequisite for understanding their breeding habitat ecology and distribution, as well as managing their habitats. Geographical information systems (GIS) and existing digital data archives provide new possibilities for the quantitative and cost-effective assessment of coastal breeding habitats of birds. We tested the applicability of GIS and digital data archives for the analysis of coastal bird habitats by conducting a multivariate analysis on the relationship between physical island characteristics and the breeding site selection of 15 species of ducks, waders, larids and alcids in 2001-2005 in the fragmented archipelago coast of south-western Finland. We used GIS and environmental databases containing shoreline, bathymetry and elevation data to calculate five physical parameters for 71 small islands and their vicinity. Island area was generally the most important factor determining the presence of the species, but also water depth, shore openness, and island elevation were important for some species. The differences and similarities in habitat preferences within and between species groups seem to reflect the breeding habitat ecology of the species. GIS and spatial data archives are becoming increasingly valuable for research and development, as well as administrative tasks. Our results indicate that physical island characteristics affect the breeding site selection and the distribution of our target species, and that GIS and digital data archives provide applicable information on the breeding habitats of coastal birds and thus function as a tool for conservation and management.